Abstract
In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of Pospiviroidae which were unknown in 1985. Indeed, individual members of Pospiviroidae consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.
Highlights
Viroids are the smallest known plant pathogens with a genome length ranging from 246 to 401 bases in size depending on the viroid species (Table S1) and variant
In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids
Viroids from the family Pospiviroidae are transcribed by DNA-dependent RNA polymerase II using the viroid RNA as a template in an asymmetric rolling circle mechanism in the nuclei of infected cells [4,5,6,7]
Summary
Viroids are the smallest known plant pathogens with a genome length ranging from 246 to 401 bases in size depending on the viroid species (Table S1) and variant. In 1985, Keese and Symons [11] proposed a model based on the secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain” [12]. These five domains, with precise borders [11,12,13], are as follows (Figure 1):
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